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mahmoodlab / SurvPath

Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction - CVPR 2024
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Data #5

Closed H-Q-N closed 7 months ago

H-Q-N commented 7 months ago

The storage location and required type of WSI do not seem to be shown in the code. If it's convenient for you, can you provide the complete data structure? Thank you very much

ajv012 commented 7 months ago

SurvPath is not meant for processing WSI. You can use the CLAM toolkit (https://github.com/mahmoodlab/CLAM) to process WSI and store the patch features in a convenient location. SurvPath is meant to be used with H&E stained WSI only.

H-Q-N commented 7 months ago

Thank you very much for your answer. What you mean is that the H&E staining wsi of tcga, as the input of the model, needs to be manually processed into a .pt file using CLAM toolbox. I can't directly use .svs as the input format of the model, right?

ajv012 commented 7 months ago

yes, that is correct. WSI (.svs) are too large in size to work with directly, so you need to process them using CLAM (or any other similar toolkit) before you use SurvPath. This is outlined in detail in the README, please refer to that for further questions.